{-| Encodes a table of amino acid properties.
Based on Livingstone & Barton, CABIOS, 9, 745-756, 1993, as seen at:
http://www.compbio.dundee.ac.uk/user/ws-dev1/jalview/latest/help/html/misc/aaproperties.html NB: based on the graphic, not the table (in which P is polar, but T is not)
|-}moduleBio.Sequence.AminoPropertieswhereimportPreludehiding(or)importBio.Sequence.SeqDatatypeAAProp=Amino->BooloneOf=flipelemorfg=\x->fx||gxaliphatic,aromatic,hydrophobic,polar,small,tiny,charged,negative,positive::AAProp-- NB: Cysteine has two variants: C s-s (small, non-polar) and C s-h (tiny, polar)-- http://www.russell.embl-heidelberg.de/aas/aas.htmlaliphatic=oneOf[Ile,Leu,Val]aromatic=oneOf[Phe,Tyr,Trp,His]hydrophobic=aromatic`or`aliphatic`or`oneOf[Cys,Ala,Gly,Thr,Met,Lys]polar=charged`or`oneOf[Asn,Ser,Thr,Tyr,Trp,Gln]-- and C s-hsmall=tiny`or`oneOf[Pro,Cys,Val,Thr,Asp,Asn]-- +Asx?tiny=oneOf[Ala,Gly,Ser]-- C s-hcharged=negative`or`positivenegative=oneOf[Asp,Glu]positive=oneOf[Lys,His,Arg]-- Based on Kyte and Doolittle, according to Wikipediahydropathy::Amino->Doublehydropathyx=casexofAla->1.8Arg->-4.5Asn->-3.5Asp->-3.5Cys->2.5Gln->-3.5Glu->-3.5Gly->-0.4His->-3.2Ile->4.5Leu->3.8Lys->-3.9Met->1.9Phe->2.8Pro->-1.6Ser->-0.8Thr->-0.7Trp->-0.9Tyr->-1.3Val->4.2_->0mass::Amino->Doublemassx=casexof-- tinyGly->57.021464Ala->71.037114Ser->87.032029-- smallPro->97.052764Val->99.068414Thr->101.04768Cys->103.00919Asn->114.04293Asp->115.02694Leu->113.08406Ile->113.08406Gln->128.05858Lys->128.09496Glu->129.04259Met->131.04048His->137.05891Phe->147.06841Arg->156.10111Tyr->163.06333Trp->186.07931_->0-- | The propensities for forming secondary structures-- From Zvelebil and Baum: Understanding Bioinformatics, Chapter 11-- citing Chou and Fasman.-- Today, more complex methods like GOR are recommended instead.helixP,strandP::Amino->DoublehelixPx=casexofAla->1.42Cys->0.70Asp->1.01Glu->1.51Phe->1.13Gly->0.61His->1.00Ile->1.08Lys->1.16Leu->1.21Met->1.45Asn->0.67Pro->0.57Gln->1.11Arg->0.98Ser->0.77Thr->0.83Val->1.06Trp->1.08Tyr->0.69_->0-- sensible?strandPx=casexofAla->0.83Cys->1.19Asp->0.54Glu->0.37Phe->1.38Gly->0.75His->0.87Ile->1.60Lys->0.74Leu->1.30Met->1.05Asn->0.89Pro->0.55Gln->1.10Arg->0.93Ser->0.75Thr->1.19Val->1.70Trp->1.37Tyr->1.40_->0